12-118197101-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016281.4(TAOK3):c.1194+1950G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,062 control chromosomes in the GnomAD database, including 1,204 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1204 hom., cov: 32)
• Consequence: TAOK3 NM_016281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

Genes affected

TAOK3 (HGNC:18133): (TAO kinase 3) The protein encoded by this gene is a serine/threonine protein kinase that activates the p38/MAPK14 stress-activated MAPK cascade but inhibits the basal activity of the MAPK8/JNK cascade. The encoded protein is a member of the GCK subfamily of STE20-like kinases. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAOK3	NM_016281.4	c.1194+1950G>A		intron_variant		ENST00000392533.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAOK3	ENST00000392533.8	c.1194+1950G>A		intron_variant		1	NM_016281.4	P1
TAOK3	ENST00000419821.6	c.1194+1950G>A		intron_variant		1		P1
TAOK3	ENST00000537305.5	n.1875+1950G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18464 AN: 151944 Hom.: 1203 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.0581

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.102

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.121 AC: 18464 AN: 152062 Hom.: 1204 Cov.: 32 AF XY: 0.119 AC XY: 8875 AN XY: 74328

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.0590

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.103

Alfa AF: 0.130 Hom.: 1376

Bravo AF: 0.115

Asia WGS AF: 0.0360 AC: 123 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.83
Dann	Benign	0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10507286; hg19: chr12-118634906;